SAXSdb — 1y79

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidyl-Dipeptidase Dcp

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 LYSINE × 1 TRYPTOPHAN × 1 GLYCINE × 1 ASPARTIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–680； UniProt 1–680

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1y79
Deposition date deposition_date	2004-12-08
Structure title title	Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor
Keywords keywords	hinge bending; peptidyl dipeptidase; carboxypeptidase; Dcp; neurolysin; ACE, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1y79__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1y79__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y79__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.23 Å
Rg (electron density)	25.07 Å
Total Rg	26.02 Å
Atom count	5506
Residues	680
Excluded volume	97254 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y79__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Peptidyl-Dipeptidase Dcp
Molecular weight formula_weight	77469.3 kDa
EC 编号 ec_number	3.4.15.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	6135

TTMNPFLVQSTLPYLAPHFDQIANHHYRPAFDEGMQQKRAEIAAIALNPQMPDFNNTILALEQSGELLTRVTSVFFAMTAAHTNDELQRLDEQFSAELAELANDIYLNGELFARVDAVWQRRESLGLDSESIRLVEVIHQRFVLAGAKLAQADKAKLKVLNTEAATLTSQFNQRLLAANKSGGLVVNDIAQLAGMSEQEIALAAEAAREKGLDNKWLIPLLNTTQQPALAEMRDRATREKLFIAGWTRAEKNDANDTRAIIQRLVEIRAQQATLLGFPHYAAWKIADQMAKTPEAALNFMREIVPAARQRASDELASIQAVIDKQQGGFSAQPWDWAFYAEQVRREKFDLDEAQLKPYFELNTVLNEGVFWTANQLFGIKFVERFDIPVYHPDVRVWEIFDHNGVGLALFYGDFFARDSKSGGAWMGNFVEQSTLNKTHPVIYNVCNYQKPAAGEPALLLWDDVITLFHEFGHTLHGLFARQRYATLSGTNTPRDFVEFPSQINEHWATHPQVFARYARHYQSGAAMPDELQQKMRNASLFNKGYEMSELLSAALLDMRWHCLEENEAMQDVDDFELRALVAENMDLPAIPPRYRSSYFAHIFGGGYAAGYYAYLWTQMLADDGYQWFVEQGGLTRENGLRFREAILSRGNSEDLERLYRQWRGKAPKIMPMLQHRGLNI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	629

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	1y79101
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	63.408 Å
Unit-cell length b length_b	67.921 Å
Unit-cell length c length_c	153.591 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2403
R_work r_work	0.2140
R_free r_free	0.2747

Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidyl-Dipeptidase Dcp

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1y79__assembly_1__model_1

1y79__assembly_1__model_1 | I(q)

1y79__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidyl-Dipeptidase Dcp

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1y79__assembly_1__model_1

1y79__assembly_1__model_1 | I(q)

1y79__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)